Funny, after my LX450 Burnt up, I was looking into a 1st gen 4 runner, and was thinking about how to put a flippac on one.
I think you have the right idea, but I'd modify it a little bit. Cut the 4 runner top to leave all the matting surfaces like you said. Then as you planned, cut the flippac to match as close as you can. At this point, I'd take some 1/8" x 3" aluminum plate. Attach it to the 4-runner toper. I'd probably drill through the topper and bolt it. Then do the same on the flippac. Now the two pieces are firmly attached to one another. Glass over the aluminum spars everywhere except where the bolts are. Now, you can take the bolts out and you're two pieces are still together. If the flip-pac is too long, just cut it so it goes over the cab. You can foam and glass it to match up (see link below on foam and fiberglass)
At this point, you just need to fill the gap. If it's a nice flat gap you can put some aluminum foil over boards or something, on the inside and glass from the outside, then remove the boards. If it's not nice and even and flat (more likely), get some foam from lowes or home depot - the house insulation foam (
http://www.rqriley.com/frp-foam.htm ) and attach it to the two toppers. Either glue it. or tape it securely - glue would be my 1st choice, double side tape second, just taping the edges would be my last choice.
The foam is flexable and will give a nice contour betwen the two toppers. Glass it from the outside - make sure you've sanded back far enough on both of them that you can get some overlap for strength. The aluminum spars will help with the strength though. You can now either glass over the foam on the inside (pick a thin foam - it comes from like 1/4" up to 3") or you can grab a scraper and pull the foam off, it'll be a bit of a mess, but not too bad. Then glass the inside after you have all the foam off. Paint the interior with bedliner and you're golden.

You don't have to do the bedliner, but if you do you have to do next to no prep work compared to trying to sand all the fiberglassing you just did to a paintable smoothness.
My ultimate idea for a 4 runner was to do what you're doing, then make a trailer out of a 4 runner bed as well. Cut it just in front of where the toper mates. Why? Well, the acid fueled idea was I could put the topper on the 4 runner, and have a canvas toneau for the trailer. Drive out to Moab in a nice quite hard topped 4 runner, while pulling a low profile trailer. Then, once in moab, throw the bikini top on the 4 runner, and put the topper on the trailer and have a nice base camp. So, for some trips you could just have the 4 runner /camper, other trips, you could have the 4 runner plus a camper trailer. Just a rambling dream....